There are two commercial versions now available:
1. WebAsyst Shop-Script: http://old.webasyst.net/shop/ – previous generation
2. Shop-Script 5: http://www.shop-script.com – newest generation
You purchased the first one (WebAsyst Shop-Script), and you are absolutely licensed to use the software.
Shop-Script 5 is a new completely new product with newer user interface and backend engine. If you want to run on the newer generation, you need to purchase it separately. We offer upgrade to the newer...

This article should help you understand what is required to open an online store with Shop-Script 5: http://www.shop-script.com/how-to-create-an-online-store/
Knowledge of PHP is not required unless you are planning to write plugins for your online store which are not yet available in our Webasyst Store: http://www.webasyst.com/store/plugins/shop/
Some basic knowledge of HTML and CSS would be helpful for editing design themes, but the available free themes (http://www.webasyst.com/store/themes/) do...

The all-new Helpdesk app is coming soon - in just one or two months!
Project management apps are in plans, but for now there is no ETA disclosed for those.
As for the support of the previous generation of WebAsyst apps (old.webasyst.net), we will continue to provide support and critical bug-fix updates even when older products become out of sale. We will announce when the support for the previous generation is over. I think it will be no less than in an year or so.